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%\documentclass[12pt]{report} % THESIS
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 %\usepackage{overcite}%reference number as an exponent NO mario 05
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\makeindex
% compile with >makeindex main

\title{\Huge \textbf{BRAHMS}\\\bigskip
{\em User Manual}}

\author{Mario Orsi}
\begin{document}

\maketitle
%\raggedright

%\include{title}

%\pagebreak
%\newpage
%\onehalfspacing
\pagenumbering{roman}\setcounter{page}{1}

%\clearpage


\include{acknowledgement}
\tableofcontents 
%\clearpage 
\listoffigures
\listoftables
%\newpage
%\openup=10pt
\pagenumbering{arabic}\setcounter{page}{1}
%\include{styleRules}
\include{introduction}
\part{Running Brahms}

%\include{gettingStarted}
\include{input/inputParameters}
\include{runningSimulations/run}
\include{output/out}
\include{visualization/vis}
\include{analysis/an}
\include{bench/benchmarks}

\part{Background}

%\include{multiResolution/multi}

%\appendix

\include{md/md}
\include{biophys/biophys}

%\part*{Appendices}

%\begin{footnotesize}
\begin{scriptsize}
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\bibliography{/home/orsi/biblio.bib}
%\end{small}
%\end{footnotesize}
%\printindex
\end{scriptsize}
%\include{coda}
\end{document},
